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Magnesium in PDB 5orj: The Crystal Structure of CK2ALPHA in Complex with Compound 3

Enzymatic activity of The Crystal Structure of CK2ALPHA in Complex with Compound 3

All present enzymatic activity of The Crystal Structure of CK2ALPHA in Complex with Compound 3:
2.7.11.1;

Protein crystallography data

The structure of The Crystal Structure of CK2ALPHA in Complex with Compound 3, PDB code: 5orj was solved by P.Brear, C.De Fusco, J.Iegre, M.Yoshida, S.Mitchell, M.Rossmann, L.Carro, H.Sore, M.Hyvonen, D.Spring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 1.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 64.790, 68.597, 333.660, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.1

Other elements in 5orj:

The structure of The Crystal Structure of CK2ALPHA in Complex with Compound 3 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of CK2ALPHA in Complex with Compound 3 (pdb code 5orj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Crystal Structure of CK2ALPHA in Complex with Compound 3, PDB code: 5orj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5orj

Go back to Magnesium Binding Sites List in 5orj
Magnesium binding site 1 out of 5 in the The Crystal Structure of CK2ALPHA in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of CK2ALPHA in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:55.3
occ:1.00
 O2B B:ADP403 2.2 72.7 1.0
O2A B:ADP403 2.3 72.2 1.0
OD1 B:ASN161 2.4 43.8 1.0
OD2 B:ASP175 2.4 58.6 1.0
CG B:ASP175 3.3 54.8 1.0
CG B:ASN161 3.4 47.4 1.0
PB B:ADP403 3.5 74.4 1.0
PA B:ADP403 3.7 70.6 1.0
CB B:ASP175 3.8 42.6 1.0
ND2 B:ASN161 3.8 39.3 1.0
O3A B:ADP403 3.9 71.5 1.0
O1B B:ADP403 4.0 72.9 1.0
OD1 B:ASP175 4.3 55.6 1.0
CE B:LYS158 4.5 59.9 1.0
O1A B:ADP403 4.6 66.0 1.0
O5' B:ADP403 4.6 68.5 1.0
C5' B:ADP403 4.6 68.0 1.0
O3' B:ADP403 4.7 68.0 1.0
CB B:ASN161 4.8 44.1 1.0
O B:HIS160 4.8 49.4 1.0
O3B B:ADP403 4.8 75.9 1.0
OD2 B:ASP156 4.8 50.9 1.0
NZ B:LYS158 5.0 65.3 1.0

Magnesium binding site 2 out of 5 in 5orj

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Magnesium binding site 2 out of 5 in the The Crystal Structure of CK2ALPHA in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of CK2ALPHA in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:55.4
occ:1.00
 O1A B:ADP403 2.8 66.0 1.0
N B:ASP175 2.9 41.6 1.0
CA B:ASP175 3.4 41.6 1.0
CZ B:PHE113 3.6 47.6 1.0
CB B:ILE174 3.8 41.1 1.0
CE2 B:PHE113 3.9 50.1 1.0
NZ B:LYS68 3.9 79.9 1.0
C B:ILE174 4.0 45.0 1.0
CE1 B:PHE113 4.1 48.4 1.0
CB B:ASP175 4.2 42.6 1.0
PA B:ADP403 4.2 70.6 1.0
CD B:LYS68 4.3 69.8 1.0
CA B:ILE174 4.3 39.4 1.0
N7 B:ADP403 4.4 59.8 1.0
OE2 B:GLU81 4.5 48.3 1.0
CE B:LYS68 4.5 74.4 1.0
CD2 B:PHE113 4.5 46.8 1.0
C B:ASP175 4.6 43.8 1.0
CD1 B:ILE174 4.6 44.0 1.0
N B:TRP176 4.6 40.4 1.0
CG1 B:ILE174 4.6 39.0 1.0
CG2 B:ILE174 4.6 40.9 1.0
CG2 B:ILE95 4.7 42.4 1.0
CD1 B:PHE113 4.8 47.2 1.0
C8 B:ADP403 4.8 63.1 1.0
OD1 B:ASP175 4.9 55.6 1.0
O2A B:ADP403 4.9 72.2 1.0
CG B:PHE113 5.0 45.9 1.0
CG B:ASP175 5.0 54.8 1.0

Magnesium binding site 3 out of 5 in 5orj

Go back to Magnesium Binding Sites List in 5orj
Magnesium binding site 3 out of 5 in the The Crystal Structure of CK2ALPHA in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of CK2ALPHA in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:52.3
occ:1.00
 O2A A:ADP404 2.6 45.7 1.0
N A:ASP175 2.9 31.6 1.0
O A:HOH501 3.0 35.5 1.0
CA A:ASP175 3.3 30.8 1.0
CZ A:PHE113 3.7 37.4 1.0
NZ A:LYS68 3.8 49.1 1.0
CB A:ILE174 3.8 29.9 1.0
CE2 A:PHE113 3.9 38.1 1.0
PA A:ADP404 4.0 48.7 1.0
C A:ILE174 4.1 33.3 1.0
CD A:LYS68 4.1 44.4 1.0
CB A:ASP175 4.2 31.3 1.0
N7 A:ADP404 4.3 41.0 1.0
CE1 A:PHE113 4.3 36.7 1.0
CA A:ILE174 4.3 27.8 1.0
CE A:LYS68 4.4 56.4 1.0
CD1 A:ILE174 4.5 33.0 1.0
OE2 A:GLU81 4.5 43.8 1.0
CD2 A:PHE113 4.5 35.7 1.0
C A:ASP175 4.6 33.6 1.0
CG1 A:ILE174 4.6 30.6 1.0
N A:TRP176 4.6 30.3 1.0
C8 A:ADP404 4.6 40.6 1.0
O1A A:ADP404 4.7 41.9 1.0
CG2 A:ILE174 4.7 27.7 1.0
O5' A:ADP404 4.7 47.8 1.0
OD1 A:ASP175 4.8 45.9 1.0
CG A:ASP175 4.9 42.9 1.0
CD1 A:PHE113 4.9 38.1 1.0
CG2 A:ILE95 4.9 34.6 1.0

Magnesium binding site 4 out of 5 in 5orj

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Magnesium binding site 4 out of 5 in the The Crystal Structure of CK2ALPHA in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of CK2ALPHA in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:76.7
occ:1.00
 CD2 A:TYR50 3.1 77.0 1.0
NZ A:LYS77 3.1 87.6 1.0
O A:HOH560 3.2 54.1 1.0
O3B A:ADP404 3.3 57.8 1.0
O A:HOH579 3.4 53.6 1.0
CA A:GLY177 3.4 32.5 1.0
OD1 A:ASP175 3.5 45.9 1.0
CE2 A:TYR50 3.5 78.3 1.0
C A:GLY177 3.6 35.6 1.0
CG A:TYR50 3.8 76.1 1.0
N A:LEU178 4.0 31.5 1.0
O A:GLY177 4.0 33.2 1.0
CG A:LEU178 4.1 40.6 1.0
N A:GLY177 4.1 32.7 1.0
CB A:TYR50 4.2 72.4 1.0
CD2 A:LEU178 4.2 47.5 1.0
CE A:LYS77 4.3 89.2 1.0
CG A:ASP175 4.4 42.9 1.0
OD2 A:ASP175 4.4 43.2 1.0
CZ A:TYR50 4.6 87.6 1.0
CD1 A:TYR50 4.7 79.1 1.0
PB A:ADP404 4.8 56.7 1.0
CA A:LEU178 4.8 31.9 1.0
CB A:LEU178 4.9 32.7 1.0
NZ A:LYS68 4.9 49.1 1.0

Magnesium binding site 5 out of 5 in 5orj

Go back to Magnesium Binding Sites List in 5orj
Magnesium binding site 5 out of 5 in the The Crystal Structure of CK2ALPHA in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of CK2ALPHA in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:37.8
occ:1.00
 O1A A:ADP404 2.2 41.9 1.0
O1B A:ADP404 2.2 49.7 1.0
OD2 A:ASP175 2.3 43.2 1.0
OD1 A:ASN161 2.4 31.3 1.0
CG A:ASP175 3.2 42.9 1.0
CG A:ASN161 3.4 39.0 1.0
PA A:ADP404 3.5 48.7 1.0
PB A:ADP404 3.5 56.7 1.0
CB A:ASP175 3.7 31.3 1.0
O3A A:ADP404 3.8 54.4 1.0
ND2 A:ASN161 3.8 30.2 1.0
O3B A:ADP404 4.0 57.8 1.0
OD1 A:ASP175 4.2 45.9 1.0
O5' A:ADP404 4.4 47.8 1.0
O3' A:ADP404 4.4 53.5 1.0
O2A A:ADP404 4.5 45.7 1.0
C5' A:ADP404 4.5 49.9 1.0
CE A:LYS158 4.6 41.6 1.0
CB A:ASN161 4.7 27.7 1.0
OD2 A:ASP156 4.8 42.6 1.0
O2B A:ADP404 4.8 57.9 1.0
O A:HIS160 4.8 36.7 1.0
C3' A:ADP404 5.0 50.4 1.0

Reference:

J.Iegre, P.Brear, C.De Fusco, M.Yoshida, S.L.Mitchell, M.Rossmann, L.Carro, H.F.Sore, M.Hyvonen, D.R.Spring. Second-Generation CK2 Alpha Inhibitors Targeting the Alpha D Pocket. Chem Sci V. 9 3041 2018.
ISSN: ISSN 2041-6520
PubMed: 29732088
DOI: 10.1039/C7SC05122K
Page generated: Mon Sep 30 01:08:08 2024

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